Merge branch 'master' into async-file-vault

scalableminds · Nov 12, 2024 · 28ddb66 · 28ddb66
2 parents 8dbd347 + 8dec578
commit 28ddb66
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Showing 10 changed files with 26 additions and 16 deletions.
diff --git a/CHANGELOG.unreleased.md b/CHANGELOG.unreleased.md
@@ -36,6 +36,7 @@ For upgrade instructions, please check the [migration guide](MIGRATIONS.released
 - Fix that scrolling in the trees and segments tab did not work while dragging. [#8162](https://github.com/scalableminds/webknossos/pull/8162)
 - Fixed that uploading a dataset which needs a conversion failed when the angstrom unit was configured for the conversion. [#8173](https://github.com/scalableminds/webknossos/pull/8173)
 - Fixed that the skeleton search did not automatically expand groups that contained the selected tree [#8129](https://github.com/scalableminds/webknossos/pull/8129)
+- Fixed interactions in the trees and segments tab like the search due to a bug introduced by [#8162](https://github.com/scalableminds/webknossos/pull/8162). [#8186](https://github.com/scalableminds/webknossos/pull/8186)
 - Fixed a bug that zarr streaming version 3 returned the shape of mag (1, 1, 1) / the finest mag for all mags. [#8116](https://github.com/scalableminds/webknossos/pull/8116)
 - Fixed sorting of mags in outbound zarr streaming. [#8125](https://github.com/scalableminds/webknossos/pull/8125)
 - Fixed a bug where you could not create annotations for public datasets of other organizations. [#8107](https://github.com/scalableminds/webknossos/pull/8107)
@@ -44,6 +45,7 @@ For upgrade instructions, please check the [migration guide](MIGRATIONS.released
 - Removed unnecessary scrollbars in skeleton tab that occurred especially after resizing. [#8148](https://github.com/scalableminds/webknossos/pull/8148)
 - Deleting a bounding box is now possible independently of a visible segmentation layer. [#8164](https://github.com/scalableminds/webknossos/pull/8164)
 - S3-compliant object storages can now be accessed via HTTPS. [#8167](https://github.com/scalableminds/webknossos/pull/8167)
+- Fixed that skeleton tree nodes were created with the wrong mag. [#8185](https://github.com/scalableminds/webknossos/pull/8185)
 - Fixed a layout persistence bug leading to empty viewports, triggered when switching between orthogonal, flight, or oblique mode. [#8177](https://github.com/scalableminds/webknossos/pull/8177)
 
 ### Removed

diff --git a/frontend/javascripts/oxalis/model/helpers/nml_helpers.ts b/frontend/javascripts/oxalis/model/helpers/nml_helpers.ts
@@ -412,7 +412,7 @@ function serializeNodes(
       rotY: node.rotation[1],
       rotZ: node.rotation[2],
       inVp: node.viewport,
-      inMag: node.mag,
+      inMag: node.resolution,
       bitDepth: node.bitDepth,
       interpolation: node.interpolation,
       time: node.timestamp,
@@ -963,7 +963,7 @@ export function parseNml(nmlString: string): Promise<{
               }),
               bitDepth: _parseInt(attr, "bitDepth", { defaultValue: DEFAULT_BITDEPTH }),
               viewport: _parseInt(attr, "inVp", { defaultValue: DEFAULT_VIEWPORT }),
-              mag: _parseInt(attr, "inMag", { defaultValue: DEFAULT_RESOLUTION }),
+              resolution: _parseInt(attr, "inMag", { defaultValue: DEFAULT_RESOLUTION }),
               radius: _parseFloat(attr, "radius", { defaultValue: Constants.DEFAULT_NODE_RADIUS }),
               timestamp: _parseTimestamp(attr, "time", { defaultValue: DEFAULT_TIMESTAMP }),
             };

diff --git a/frontend/javascripts/oxalis/model/reducers/skeletontracing_reducer_helpers.ts b/frontend/javascripts/oxalis/model/reducers/skeletontracing_reducer_helpers.ts
@@ -146,7 +146,7 @@ export function createNode(
     radius,
     rotation,
     viewport,
-    mag: resolution,
+    resolution,
     id: nextNewId,
     timestamp,
     bitDepth: state.datasetConfiguration.fourBit ? 4 : 8,
@@ -846,7 +846,7 @@ function serverNodeToMutableNode(n: ServerNode): MutableNode {
     rotation: Utils.point3ToVector3(n.rotation),
     bitDepth: n.bitDepth,
     viewport: n.viewport,
-    mag: n.resolution,
+    resolution: n.resolution,
     radius: n.radius,
     timestamp: n.createdTimestamp,
     interpolation: n.interpolation,

diff --git a/frontend/javascripts/oxalis/model/sagas/proofread_saga.ts b/frontend/javascripts/oxalis/model/sagas/proofread_saga.ts
@@ -270,7 +270,7 @@ function* createEditableMapping(): Saga<string> {
   // Get volume tracing again to make sure the version is up to date
   const upToDateVolumeTracing = yield* select((state) => getActiveSegmentationTracing(state));
   if (upToDateVolumeTracing == null) {
-    throw new Error("No active segmentation tracing layer. Cannot create editble mapping.");
+    throw new Error("No active segmentation tracing layer. Cannot create editable mapping.");
   }
 
   const volumeTracingId = upToDateVolumeTracing.tracingId;

diff --git a/frontend/javascripts/oxalis/store.ts b/frontend/javascripts/oxalis/store.ts
@@ -89,7 +89,7 @@ export type MutableNode = {
   rotation: Vector3;
   bitDepth: number;
   viewport: number;
-  mag: number;
+  resolution: number;
   radius: number;
   timestamp: number;
   interpolation: boolean;

diff --git a/frontend/javascripts/oxalis/view/right-border-tabs/connectome_tab/connectome_view.tsx b/frontend/javascripts/oxalis/view/right-border-tabs/connectome_tab/connectome_view.tsx
@@ -163,7 +163,7 @@ const synapseNodeCreator = (synapseId: number, synapsePosition: Vector3): Mutabl
   radius: Constants.DEFAULT_NODE_RADIUS,
   rotation: [0, 0, 0],
   viewport: 0,
-  mag: 0,
+  resolution: 0,
   id: synapseId,
   timestamp: Date.now(),
   bitDepth: 8,

diff --git a/frontend/javascripts/oxalis/view/right-border-tabs/scrollable_virtualized_tree.tsx b/frontend/javascripts/oxalis/view/right-border-tabs/scrollable_virtualized_tree.tsx
@@ -1,7 +1,7 @@
 import { Tree as AntdTree, type TreeProps } from "antd";
 import type { BasicDataNode } from "antd/es/tree";
 import { throttle } from "lodash";
-import { useCallback, useRef } from "react";
+import { forwardRef, useCallback, useRef } from "react";
 import type RcTree from "rc-tree";
 
 const MIN_SCROLL_SPEED = 30;
@@ -10,8 +10,10 @@ const MIN_SCROLL_AREA_HEIGHT = 60;
 const SCROLL_AREA_RATIO = 10; // 1/10th of the container height
 const THROTTLE_TIME = 25;
 
-function ScrollableVirtualizedTree<T extends BasicDataNode>(
-  props: TreeProps<T> & { ref: React.RefObject<RcTree> },
+// React.forwardRef does not support generic types, so we need to define the type of the ref separately.
+function ScrollableVirtualizedTreeInner<T extends BasicDataNode>(
+  props: TreeProps<T>,
+  ref: React.Ref<RcTree>,
 ) {
   const wrapperRef = useRef<HTMLDivElement>(null);
   // biome-ignore lint/correctness/useExhaustiveDependencies: biome is not smart enough to notice that the function needs to be re-created when wrapperRef changes.
@@ -56,9 +58,15 @@ function ScrollableVirtualizedTree<T extends BasicDataNode>(
 
   return (
     <div ref={wrapperRef}>
-      <AntdTree {...props} onDragOver={onDragOver} />
+      <AntdTree {...props} onDragOver={onDragOver} ref={ref} />
     </div>
   );
 }
 
+const ScrollableVirtualizedTree = forwardRef(ScrollableVirtualizedTreeInner) as <
+  T extends BasicDataNode,
+>(
+  props: TreeProps<T> & { ref?: React.Ref<RcTree> },
+) => ReturnType<typeof ScrollableVirtualizedTreeInner>;
+
 export default ScrollableVirtualizedTree;
diff --git a/frontend/javascripts/oxalis/view/right-border-tabs/segments_tab/segments_view.tsx b/frontend/javascripts/oxalis/view/right-border-tabs/segments_tab/segments_view.tsx
@@ -1904,7 +1904,7 @@ class SegmentsView extends React.Component<Props, State> {
                                 overflow: "hidden",
                               }}
                             >
-                              <ScrollableVirtualizedTree<SegmentHierarchyNode>
+                              <ScrollableVirtualizedTree
                                 allowDrop={this.allowDrop}
                                 onDrop={this.onDrop}
                                 onSelect={this.onSelectTreeItem}

diff --git a/frontend/javascripts/test/libs/nml.spec.ts b/frontend/javascripts/test/libs/nml.spec.ts
@@ -34,7 +34,7 @@ const createDummyNode = (id: number): Node => ({
   untransformedPosition: [id, id, id],
   additionalCoordinates: [],
   radius: id,
-  mag: 10,
+  resolution: 10,
   rotation: [id, id, id],
   timestamp: id,
   viewport: 1,

diff --git a/frontend/javascripts/test/reducers/skeletontracing_reducer.spec.ts b/frontend/javascripts/test/reducers/skeletontracing_reducer.spec.ts
@@ -130,7 +130,7 @@ test("SkeletonTracing should add a new node", (t) => {
     untransformedPosition: position,
     rotation,
     viewport,
-    mag: resolution,
+    resolution,
     id: 1,
     radius: 1,
   });
@@ -295,7 +295,7 @@ test("SkeletonTracing should delete nodes and split the tree", (t) => {
     untransformedPosition: [0, 0, 0],
     additionalCoordinates: null,
     radius: 10,
-    mag: 10,
+    resolution: 10,
     rotation: [0, 0, 0],
     timestamp: 0,
     viewport: 1,
@@ -453,7 +453,7 @@ test("SkeletonTracing should delete an edge and split the tree", (t) => {
     untransformedPosition: [0, 0, 0],
     additionalCoordinates: null,
     radius: 10,
-    mag: 10,
+    resolution: 10,
     rotation: [0, 0, 0],
     timestamp: 0,
     viewport: 1,